Re: [QE-users] DFPT of thin metal layer: convergence has not been achieved
Hi,
As 'smearing' value is not given, so I suppose you used default Gaussian
smearing with spreading 0.001 Ry.
For a better convergence in metallic system, I would suggest (no
warranty) you try other smearing method
like Methfessel-Paxton or Marzari-Vanderbilt cold smearing with a little
high value of smearing width, say, 0.01 or 0.02 Ry and use discussions from
http://theossrv1.epfl.ch/Main/ElectronicTemperature
to judge the convergence of parameters you are interested in.
With best regards,
Duc-Long
PhD student,
Academia Sinica, Taiwan
On 11/09/2018 02:13 PM, Christoph Wolf wrote:
Dear all,
after reading your comments I have tried the following:
- three different Pseudos ("just to make sure..") that all work in the
bulk
- increasing the layer numbers 6,7,8,9 ML
- test if the vacuum distance has any difference (but apparently it
does not in the range of 10-20A).
but for Cu(111) none of these works in the ph.x electric fields
calculation. I have attached the run script, maybe someone could give
it a quick glance? I guess the surface state splitting plays a minor
role in this general convergence issue..
Thank you for your help in this matter it is very much appreciated!
Best,
Chris
--
Postdoctoral Researcher
Center for Quantum Nanoscience, Institute for Basic Science
Ewha Womans University, Seoul, South Korea
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Re: [QE-users] NON CONVERGENCE OF PHONON CALCULATION DUE TO LIMITED NUMBER OF ITERATIONSR
Dear Shuham, After modifying maxter from 100 to 300, you should recompile ph.x (type make in folder PHonon/PH) as I can see the loop stopped after 100 iterations. Adding to those comments from Dr. Mattioli and Dr. Wolf, you may want to reduce 'alpha_mix' to get better convergence. H.T.H Duc-Long Nguyen Graduate student, TIGP, Academia Sinica, Taiwan On 10/04/2018 11:42 PM, Shubham Tyagi wrote: Respected Sir/Ma'am I am Shubham Tyagi. I m currently pursuing masters in science(Physics) from IIT Jodhpur, India. I have taken DFT as my topic for my second-year project. Now I am facing some difficulties regarding that. The difficulty is summed as: I was doing phonon calculation for a supercell and I encountered with a problem that the calculations did not converge as the maximum iteration was till 100 only. I tried changing the maxter from 100 to 300 but all in vain. This all was for phonon calculation. So can you provide me with some way to increase the number of iterations for phonon calculation? The required files are attached On Thu, Oct 4, 2018 at 1:57 PM Giuseppe Mattioli mailto:giuseppe.matti...@ism.cnr.it>> wrote: Dear Colleague First of all please sign your posts to this forum with name and scientific affiliation. It's impossible to help you if you do not provide any detail of your calculation. pw.x and ph.x input files are necessary to check if one (among many) critical parameter is likely responsible for your convergence difficulties. This does not imply, of course, that ALL convergence difficulties can be overcome... HTH Giuseppe Shubham Tyagi mailto:shubhamtyagi...@gmail.com>> ha scritto: > Respected Sir/Ma'am > I was doing phonon calculation for a supercell and I encountered with a > problem that the calculations did not converge as the maximum iteration was > till 100 only. > I tried changing the maxter from 100 to 300 but all in vain. This all was > for phonon calculation. So can you provide me with some way to increase the > number of iterations for phonon calculation? GIUSEPPE MATTIOLI CNR - ISTITUTO DI STRUTTURA DELLA MATERIA Via Salaria Km 29,300 - C.P. 10 I-00015 - Monterotondo Scalo (RM) Mob (*preferred*) +39 373 7305625 Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: mailto:giuseppe.matti...@ism.cnr.it>> ___ users mailing list users@lists.quantum-espresso.org <mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] ERROR(FoX) when executing crossing nodes
Dear all, Since the release of QE 6.2.1 I encountered the error message as following when executing parallel pw.x on multi nodes: - ERROR(FoX) Cannot open file - There is no errors when running parallel on single node with the same input file. I did not encounter this error using previous version of QE like 6.2, 5.4.0 with the same make.inc (or make.sys). Attached please find the make.inc and the output file. With best regards, Duc-Long -- Duc-Long Nguyen PhD Student, Molecular Science and Technology Program, TIGP Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan Phone +886-979279073 scf.out Description: Binary data # make.inc. Generated from make.inc.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # $(CPP) $(CPPFLAGS) $< -o $*.F90 # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< # Top QE directory, useful for locating libraries, linking QE with plugins # The following syntax should always point to TOPDIR: TOPDIR = $(dir $(abspath $(filter %make.inc,$(MAKEFILE_LIST # if it doesn't work, uncomment the following line (edit if needed): # TOPDIR = /home/dlnguyen/bin/qe-6.2 # DFLAGS = precompilation options (possible arguments to -D and -U) # used by the C compiler and preprocessor # To use libxc (v>=3.0.1), add -D__LIBXC to DFLAGS # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas # MANUAL_DFLAGS = additional precompilation option(s), if desired # BEWARE: it does not work for IBM xlf! Manually edit FDFLAGS MANUAL_DFLAGS = DFLAGS = -D__DFTI -D__MPI -D__SCALAPACK FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS) # IFLAGS = how to locate directories with *.h or *.f90 file to be included # typically -I$(TOPDIR)/include -I/some/other/directory/ # the latter contains .e.g. files needed by FFT libraries # for libxc add -I/path/to/libxc/include/ IFLAGS = -I$(TOPDIR)/include -I$(TOPDIR)/FoX/finclude -I$(TOPDIR)/S3DE/iotk/include/ -I/opt/intel/Compiler/11.1/056/mkl/include # MOD_FLAG = flag used by f90 compiler to locate modules MOD_FLAG = -I # BASEMOD_FLAGS points to directories containing basic modules, # while BASEMODS points to the corresponding module libraries # Each Makefile can add directories to MODFLAGS and libraries to QEMODS BASEMOD_FLAGS= $(MOD_FLAG)/$(TOPDIR)/iotk/src \ $(MOD_FLAG)/$(TOPDIR)/Modules \ $(MOD_FLAG)/$(TOPDIR)/FFTXlib \ $(MOD_FLAG)/$(TOPDIR)/LAXlib \ $(MOD_FLAG)/$(TOPDIR)/UtilXlib \ $(MOD_FLAG)/$(TOPDIR)/FoX/finclude # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90 = mpif90 F90 = ifort CC = mpicc F77= mpif77 # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP= cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O2 -assume byterecl -g -traceback # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback # compiler flag needed by some compilers when the main program is not fortran # Currently used for Yambo FFLAGS_NOMAIN = -nofor_main # Linker, linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty # for libxc, set LD_LIBS=-L/path/to/libxc/lib/ -lxcf90 -lxc LD = mpif90 LDFLAGS= -static-intel LD_LIBS= # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy via "--with
[QE-users] ERROR(FoX) when executing crossing nodes
Dear all, Since the release of QE 6.2.1 I encountered the error message as following when executing parallel pw.x on multi nodes: - ERROR(FoX) Cannot open file - There is no errors when running parallel on single node with the same input file. I did not encounter this error using previous version of QE like 6.2, 5.4.0 with the same make.inc (or make.sys). Attached please find the make.inc and the output file. With best regards, Duc-Long -- Duc-Long Nguyen PhD Student, Molecular Science and Technology Program, TIGP Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan Phone +886-979279073 scf.out Description: Binary data # make.inc. Generated from make.inc.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # $(CPP) $(CPPFLAGS) $< -o $*.F90 # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< # Top QE directory, useful for locating libraries, linking QE with plugins # The following syntax should always point to TOPDIR: TOPDIR = $(dir $(abspath $(filter %make.inc,$(MAKEFILE_LIST # if it doesn't work, uncomment the following line (edit if needed): # TOPDIR = /home/dlnguyen/bin/qe-6.2 # DFLAGS = precompilation options (possible arguments to -D and -U) # used by the C compiler and preprocessor # To use libxc (v>=3.0.1), add -D__LIBXC to DFLAGS # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas # MANUAL_DFLAGS = additional precompilation option(s), if desired # BEWARE: it does not work for IBM xlf! Manually edit FDFLAGS MANUAL_DFLAGS = DFLAGS = -D__DFTI -D__MPI -D__SCALAPACK FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS) # IFLAGS = how to locate directories with *.h or *.f90 file to be included # typically -I$(TOPDIR)/include -I/some/other/directory/ # the latter contains .e.g. files needed by FFT libraries # for libxc add -I/path/to/libxc/include/ IFLAGS = -I$(TOPDIR)/include -I$(TOPDIR)/FoX/finclude -I$(TOPDIR)/S3DE/iotk/include/ -I/opt/intel/Compiler/11.1/056/mkl/include # MOD_FLAG = flag used by f90 compiler to locate modules MOD_FLAG = -I # BASEMOD_FLAGS points to directories containing basic modules, # while BASEMODS points to the corresponding module libraries # Each Makefile can add directories to MODFLAGS and libraries to QEMODS BASEMOD_FLAGS= $(MOD_FLAG)/$(TOPDIR)/iotk/src \ $(MOD_FLAG)/$(TOPDIR)/Modules \ $(MOD_FLAG)/$(TOPDIR)/FFTXlib \ $(MOD_FLAG)/$(TOPDIR)/LAXlib \ $(MOD_FLAG)/$(TOPDIR)/UtilXlib \ $(MOD_FLAG)/$(TOPDIR)/FoX/finclude # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90 = mpif90 F90 = ifort CC = mpicc F77= mpif77 # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP= cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O2 -assume byterecl -g -traceback # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback # compiler flag needed by some compilers when the main program is not fortran # Currently used for Yambo FFLAGS_NOMAIN = -nofor_main # Linker, linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty # for libxc, set LD_LIBS=-L/path/to/libxc/lib/ -lxcf90 -lxc LD = mpif90 LDFLAGS= -static-intel LD_LIBS= # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy via "--with
Re: [Pw_forum] query
On 05/23/2017 01:30 PM, aprat...@iisermohali.ac.in wrote:
> and four P atoms of unit cell only in Angstroms
Then you may considering to put ATOMIC_POSITIONS in Angstrom not
{crystal}. You can check your unit cell first with xcrysden.
I'm not so familiar with your system but your k-point mesh may not very
accurate with respect to your unit cell.
(4x4x1 k-mesh when b is the longest lattice parameter).
Best regards,
Duc-Long
--
Duc-Long Nguyen
Graduate Student, Molecular Science and Technology Program, TIGP
Institute of Atomic and Molecular Sciences,
Academia Sinica, Taipei 106, Taiwan
Phone +886-979279073
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Re: [Pw_forum] The error when use xcrysden and run pw.x for PdxTaSe2
Dear Oanh Nguyen, Your input contains a lot of errors: + ibrav = 0 then A, B, C, cosAB, cosAC, cosBC will not be needed, CELL_PARAMETERS info is required(as you provided) A quick test by changing ibrav= 6 and remove the CELL_PARAMETER part works for me. You should check whether the cell info and atoms position are correct first. + ATOMIC_SPECIES for Pd is missing Please sign your posts by indicating your affiliation. Best regards, Duc-Long -- Duc-Long Nguyen Graduate Student, Molecular Science and Technology Program, TIGP Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan Phone +886-979279073 On 10/19/2016 11:04 AM, Oanh Nguyen wrote: I have a model PdxTaSe2 with x=0.1. I built input file with the convinient cell (62 atom - 2 Pd, 20 Ta and - 40 Se) I have bilayer in this model. So, when I use xcrysden to simulate this model, I have problems with pwixsf.f : "At line 131 of file pwixsf.f (unit=5,file='stdin'), Fortran runtime error: Bad real number initem 1 of list input" When I run pw.x to create the wave function. threr is a problem is that : "At line 1031 of file read_cards.f90 Fortran runtime error: Bad real number in item 1 of list input" But don't find two file pwixsf.f and read_cards.f90. Can you help me to fix them? Below is the input file ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Kpoints - x coordinates - reg.,
Dear Muthu, IF you take a look at the file plotband.f90 in PP/src folder, specifically from line 214-241 you can see some hints: dxmod=sqrt ( (k(1,n)-k(1,n-1))**2 + & (k(2,n)-k(2,n-1))**2 + & (k(3,n)-k(3,n-1))**2 ) kx(n) = kx(n-1) + dxmod HTH, Duc-Long -- Duc-Long Nguyen Graduate Student, Molecular Science and Technology Program, TIGP Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan Phone +886-979279073 On 06/12/2016 05:29 PM, Muthu V wrote: Dear QE'ions I used the Si example file provided in QE/PP/examples/example01/ (ie run_example) and in si.bands.out i noticed the following high-symmetry point: 0.5000 0.5000 0.5000 x coordinate 0. high-symmetry point: 0. 0. 0. x coordinate 0.8660 high-symmetry point: 0. 1. 0. x coordinate 1.8660 high-symmetry point: 1. 1. 0. x coordinate 1.8660 high-symmetry point: 0. 0. 0. x coordinate 3.2802 how the three index ( ex. 0.5 0.5 0.5 and so on) is converted into one point ( 0. 0.86660 1.8660 1.8660 3.2802). and the meaning of1.0 1.0 0.0 K_POINT in run_example file ( used in band calculation) Thank you *Muthu V * *Sri Paramakalyani College * *Alwarkurichi * *India* ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] thermo_pw 0.4 compilation error (test_colors.f90)
Dear all, I would like to ask a question regarding compilation error on thermo_pw 0.4. After successfully compiled QE.5.3.0 with intel compiler 2013 and openmpi, I use the command suggested in the user guide: make join_qe back to QE folder ./configure make thermo_pw the following error message appeared : test_colors.f90(261): error #6353: A RETURN statement is invalid in the main program. RETURN ^ compilation aborted for test_colors.f90 (code 1) Please find in the attachment my make.sys file(in txt form). I appreciate any hints that you can give. With best regards, Duc-Long Nguyen -- Duc-Long Nguyen Graduate Student, Molecular Science and Technology Program, TIGP Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan Phone +886-979279073 # make.sys. Generated from make.sys.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # $(CPP) $(CPPFLAGS) $< -o $*.F90 # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< # topdir for linking espresso libs with plugins TOPDIR = /home/jesse/bin/espresso-5.3.0 # DFLAGS = precompilation options (possible arguments to -D and -U) # used by the C compiler and preprocessor # FDFLAGS = as DFLAGS, for the f90 compiler # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas # MANUAL_DFLAGS = additional precompilation option(s), if desired # You may use this instead of tweaking DFLAGS and FDFLAGS # BEWARE: will not work for IBM xlf! Manually edit FDFLAGS MANUAL_DFLAGS = DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA -D__SCALAPACK $(MANUAL_DFLAGS) FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS) # IFLAGS = how to locate directories where files to be included are # In most cases, IFLAGS = -I../include IFLAGS = -I../include # MOD_FLAGS = flag used by f90 compiler to locate modules # Each Makefile defines the list of needed modules in MODFLAGS MOD_FLAG = -I # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90 = mpif90 #F90 = ifort CC = mpicc F77= mpif77 # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP= cpp CPPFLAGS = -P -C -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -O3 -axCORE-AVX2,SSE4.2 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O3 -axCORE-AVX2,SSE4.2 # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback # compiler flag needed by some compilers when the main is not fortran # Currently used for Yambo FFLAGS_NOMAIN = -nofor_main # Linker, linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty LD = mpif90 LDFLAGS= -static-intel LD_LIBS= # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy : # BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a # BLAS_LIBS_SWITCH = internal BLAS_LIBS = -L/opt/intel/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core BLAS_LIBS_SWITCH = external # If you have nothing better, use the local copy : # LAPACK_LIBS = /your/path/to/espresso/lapack-3.2/lapack.a # LAPACK_LIBS_SWITCH = internal # For IBM machines with essl (-D__ESSL): load essl BEFORE lapack ! # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order LAPACK_LIBS= LAPACK_LIBS_SWITCH = external ELPA_LIBS_SWITCH = disabled SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 # nothing needed here if the the internal copy of FFTW is compiled # (needs -D__
Re: [Pw_forum] Atomic positions for Black Phosphorus calculations
Hi, You could use xcrysden to check your input. This is the result with your input: Number of Atoms: 8 Number of Frames: 12 WARNING: Atom 1 and atom 3 overlap !!! Atom 3 deleted !!! WARNING: Atom 2 and atom 7 overlap !!! Atom 7 deleted !!! WARNING: Atom 4 and atom 8 overlap !!! Atom 8 deleted !!! WARNING: Atom 5 and atom 6 overlap !!! Atom 6 deleted !!! That was also why pwscf showed that error. Duc-Long On 1/12/2016 7:46 AM, Elio Physics wrote: Dear Duc-Long, thanks for your response. I do not think they have the same coordinate. The "y" coordinate of one is *0.10168* while that of the 2nd is *1.10168, * that is a difference of 1 ang. Elio *From:* pw_forum-boun...@pwscf.org on behalf of Duc-Long NGUYEN *Sent:* Monday, January 11, 2016 9:38 PM *To:* PWSCF Forum *Subject:* Re: [Pw_forum] Atomic positions for Black Phosphorus calculations Dear Elio, ATOMIC_POSITIONS crystal P -0.89832 0.89832 0.91944 P -0.39832 0.39832 0.58056 _P -0.10168 0.10168 0.08056_ P 0.10168 0.89832 0.91944 _P -0.10168 1.10168 0.08056_ P -0.60168 0.60168 0.41944 P -0.39832 1.39832 0.58056 P 0.39832 0.60168 0.41944 These two atom positions have the same coordinate. This could be the problem. Duc-Long On 1/12/2016 6:44 AM, Elio Physics wrote: Dear all, I am trying to perform some calculations on Black Phosphorus (BP). To get the atomic positions I used the Crystal Builder, where I have chosen the lattice type to be base centered orthorhombic. The "builder" produced a set of cartesian and fractional (in terms of the primitive cell vectors) . I have used the fractional ones and I have also used ibrav=0 with the CELL_PARAMETERS defined as in the builder (a/2, -b/2, 0), (a/2, b/2,0), (0,0,c). However I have got the following error: %% from check_atoms : error # 1 atoms # 1 and # 4 overlap! %% Doing the same calculation with ibrav=8 and using the coordinates produced by the Crystal builder for a simple orthorhombic does not produce any errors. Can anyone please tell me what is wrong with atoms (1) and (4). Is BP simple or base centered orthorhombic..Where can I find the coorect atomic position of bulk BP? The scf input is below: &CONTROL prefix='bp', calculation='scf', restart_mode='from_scratch', wf_collect=.true., forc_conv_thr=1.D-4 etot_conv_thr=1.D-5 tstress=.true., tprnfor=.true., pseudo_dir ='/home_cluster/fis718/elio/espresso-4.1.3/pseudo', outdir='/home_cluster/fis718/elio/espresso-4.1.3/BP/OUT' / &SYSTEM ibrav=0,celldm(1)=6.26179,nat=8, ntyp= 1, ecutwfc=10, ecutrho=40, occupations='smearing', london=.true., smearing='mp', degauss=0.035,nbnd=32 / &ELECTRONS conv_thr=1.D-8, mixing_beta=0.1 / &IONS ion_dynamics='bfgs' / &CELL cell_dynamics='bfgs' press=0.0 / ATOMIC_SPECIES P 30.97376 P.pbe-n-van.UPF ATOMIC_POSITIONS crystal P -0.89832 0.89832 0.91944 P -0.39832 0.39832 0.58056 P -0.10168 0.10168 0.08056 P 0.10168 0.89832 0.91944 P -0.10168 1.10168 0.08056 P -0.60168 0.60168 0.41944 P -0.39832 1.39832 0.58056 P 0.39832 0.60168 0.41944 K_POINTS automatic 2 2 2 0 0 0 CELL_PARAMETERS alat 0.5000 -1.58106 0. 0.500 1.58106 0. 0. 0.0 4.3763 thanks Elio Arbid University of Nottingham UK ___________ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum -- Duc-Long Nguyen Graduate Student, Molecular Science and Technology Program, TIGP Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan Phone +886 979279073 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Atomic positions for Black Phosphorus calculations
Dear Elio, ATOMIC_POSITIONS crystal P -0.89832 0.89832 0.91944 P -0.39832 0.39832 0.58056 _P -0.10168 0.10168 0.08056_ P 0.10168 0.89832 0.91944 _P -0.10168 1.10168 0.08056_ P -0.60168 0.60168 0.41944 P -0.39832 1.39832 0.58056 P 0.39832 0.60168 0.41944 These two atom positions have the same coordinate. This could be the problem. Duc-Long On 1/12/2016 6:44 AM, Elio Physics wrote: Dear all, I am trying to perform some calculations on Black Phosphorus (BP). To get the atomic positions I used the Crystal Builder, where I have chosen the lattice type to be base centered orthorhombic. The "builder" produced a set of cartesian and fractional (in terms of the primitive cell vectors) . I have used the fractional ones and I have also used ibrav=0 with the CELL_PARAMETERS defined as in the builder (a/2, -b/2, 0), (a/2, b/2,0), (0,0,c). However I have got the following error: %% from check_atoms : error # 1 atoms # 1 and # 4 overlap! %% Doing the same calculation with ibrav=8 and using the coordinates produced by the Crystal builder for a simple orthorhombic does not produce any errors. Can anyone please tell me what is wrong with atoms (1) and (4). Is BP simple or base centered orthorhombic..Where can I find the coorect atomic position of bulk BP? The scf input is below: &CONTROL prefix='bp', calculation='scf', restart_mode='from_scratch', wf_collect=.true., forc_conv_thr=1.D-4 etot_conv_thr=1.D-5 tstress=.true., tprnfor=.true., pseudo_dir ='/home_cluster/fis718/elio/espresso-4.1.3/pseudo', outdir='/home_cluster/fis718/elio/espresso-4.1.3/BP/OUT' / &SYSTEM ibrav=0,celldm(1)=6.26179,nat=8, ntyp= 1, ecutwfc=10, ecutrho=40, occupations='smearing', london=.true., smearing='mp', degauss=0.035,nbnd=32 / &ELECTRONS conv_thr=1.D-8, mixing_beta=0.1 / &IONS ion_dynamics='bfgs' / &CELL cell_dynamics='bfgs' press=0.0 / ATOMIC_SPECIES P 30.97376 P.pbe-n-van.UPF ATOMIC_POSITIONS crystal P -0.89832 0.89832 0.91944 P -0.39832 0.39832 0.58056 P -0.10168 0.10168 0.08056 P 0.10168 0.89832 0.91944 P -0.10168 1.10168 0.08056 P -0.60168 0.60168 0.41944 P -0.39832 1.39832 0.58056 P 0.39832 0.60168 0.41944 K_POINTS automatic 2 2 2 0 0 0 CELL_PARAMETERS alat 0.5000 -1.58106 0. 0.500 1.58106 0. 0. 0.0 4.3763 thanks Elio Arbid University of Nottingham UK ___________ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum -- Duc-Long Nguyen Graduate Student, Molecular Science and Technology Program, TIGP Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan Phone +886 979279073 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Problem with ph.x code after a vc-relax scf run
Dear Cameron Foss, The error shows exactly what you should notice: "The phonon code is not working after vc-relax" You should get the output position from your system after vc-relax step, run another scf (without vc-relax) , set the ibrav=0 and position the vc-relax step. After that you can run the phonon code. With best regards Duc-Long Nguyen On 7/18/2014 9:09 AM, Cameron Foss wrote: > Hello all, > > I am trying to find the phonon frequencies of silicon under > hydrostatic strain. The SCF file runs to completion, however when I > run the ph.x code it give an error saying: > "Error in routine phq_readin (1): > The phonon code is not working after vc-relax" > > Here's the scf input file > &control > calculation='vc-relax' > restart_mode='from_scratch', > outdir='../../../../OUTPUT/poster/strained', > pseudo_dir='../../../../pseudo', > prefix='hydro-silicon' > / > &system > ibrav=2, celldm(1)=10.263, nat=2, ntyp=1, > ecutwfc =20.0 > / > &electrons > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > &ions > ion_dynamics='damp' > / > &cell > cell_dynamics='damp-w', > press=35.0, > cell_dofree='all' > / > ATOMIC_SPECIES > Si 28.0855 Si.pz-vbc.UPF > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.25 0.25 0.25 > K_POINTS >10 > 0.125 0.125 0.125 1.00 > 0.125 0.125 0.375 3.00 > 0.125 0.125 0.625 3.00 > 0.125 0.125 0.875 3.00 > 0.125 0.375 0.375 3.00 > 0.125 0.375 0.625 6.00 > 0.125 0.375 0.875 6.00 > 0.125 0.625 0.625 3.00 > 0.375 0.375 0.375 1.00 > 0.375 0.375 0.625 3.00 > %%% > > here's the ph input file > &inputph >tr2_ph=1.0d-14, >ldisp=.true. >nq1=4, nq2=4, nq3=4, >amass(1)= 28.0855, >prefix='hydro-silicon' >outdir='../../../../OUTPUT/poster/strained' >fildyn='hydro-si.dyn' > / > %%%5 > > and the output of ph.x (minus the general heading information) > G-vector sticks info > > sticks: dense smooth PW G-vecs:dense smooth PW > Sum 283 283 91 3143 3143 561 > > > %% > Error in routine phq_readin (1): > The phonon code is not working after vc-relax > % > > stopping ... > > Documentation in the ph.x user guide suggests that there's a problem > with my scf run, however, I cannot seem to find the issue. Any help > would be greatly appreciated. > > Best, > Cameron Foss > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140718/de3d6f89/attachment.html
